Everyday Scientist

my world is crumbling!

What the what?!?

JACS will now consider Communications of any length up to 4 journal pages and will include the Abstract in the PDF and print versions, starting with Volume 132, issue 27 (July 14, 2010). Authors should refer to the online Information for Authors and use the Communications template when submitting Communications.

Four pages is not a letter. That’s an article, dammit. And abstracts for letters. WTF? No no no. This is all wrong.

What’s the best part of JACS Comms? That they’re short and sweet. You can actually read the damn things, instead of just reading the abstract and looking at the pretty pictures (like we all do with full articles). No longer. Now JACS Comms will be long and complex. Boo.

Instead of destroying the sanctity of the blessed JACS Comm, ACS should have added an intermediate category between Comms and Full Papers.

This is almost as bad as when ACS defaced the elegant JACS by adding images!

(Unlike FSP, I really am a curmudgeon.)

man, i’ve been really slack lately

Sorry I haven’t posted anything for such a long time. I’ve been on vacation before my postdoc starts. I’ve been out of the loop, mainly because I don’t have access to journal articles until July. The break has been nice, but I am sorta looking forward to doing some science soon!

That’s all.

more self-promotion: defense and review

First, a review of mine was just accepted:

Lord, S. J.; Lee, H. D.; Moerner, W. E. Perspective: Single-Molecule Spectroscopy and Imaging of Biomolecules in Living Cells. Anal. Chem. 2010, accepted.

Also, I successfully defended my PhD last week. :)

alivisatos

Not a surprising move, but nice that it’s finalized now. Paul Alivisatos is now the director of the Lawrence Berkeley National Lab. He’s taking Steve Chu’s old job. Good luck, Paul.

ozone hole and global weirding

Nature has a nice News Feature on how humans first caused an ozone hole in the atmosphere, then banded together to fix it. Really pretty inspiring what we can do when we need to. (The scientific story is also interesting.) And a lesson to how we can work together to solve the specter of global climate change and global weirding.

The images on the left show a computer model of what the ozone hole (blue) would have looked like if we had done nothing; the ones on the right are what we’ve (probably) done by eliminating CFCs from the atmosphere. The large ozone hole would have been seriously catastrophic: Living in NYC or Tokyo would mean getting dangerous sunburns in 5 minutes of sun exposure. Ouch.

I think the ozone hole offers two lessons. (1) That climate science is not BS. And (2) that humans can cause and solve global atmospheric problems. The first probably won’t convince any global-warming skeptic, because they could claim that it was the same faulty science then as now, and that there never was a ozone hole.

But the second lesson should inspire all but the most adamant doubters. Humans are powerful enough to dramatically alter Earth’s environment, sometimes in catastrophic ways. Moreover, we can collaborate internationally to solve global problems. Why are we not inspired to slow global weirding (and solve other international problems such as abject poverty)?

man bites dog

Former Stanford graduate student Christopher Sclimenti is suing his former PI, Prof Michele Calos, for patent infringement and plagiarism. See stories here, here, and here. The complaint can be read here.

The summary is as follows:

• Student was originally on a patent application.
• At some point, Stanford and/or prof removed student’s name from application, which becomes this patent. Prof Calos is the only inventor listed on the patent.
• Prof filed a second patent, which is a continuation of the first. Prof Calos is still the only inventor listed.
• Prof filed two other applications (here and here), still the sole inventor listed, with significant portions copied from the student’s dissertation. (Stanford Daily found about 20 paragraphs in one application that were essentially identical to paragraphs in his dissertation!)

All parties agreed to an Alternative Dispute Resolution (ADR) with a neutral party. The ADR panel concluded that the student was a co-inventor and should have been included in the patent. As a result, Stanford agreed to add him to the issued patent (but I see no evidence that that has occurred yet).

According to Stanford’s OTL page, inventorship is different than what most scientists would consider authorship. For instance, “A person who contributed only labor and/or the supervision of routine techniques, but who did not contribute to the idea—the concept of one of the embodiments of the claimed invention—is not considered an inventor.” For the prof and the University to claim that the student was not an inventor, they implied that he was only a technician and did not contribute to conceiving any of the claims in the patent. That’s possible, but the ADR panel disagreed. It seems pretty straightforward that the student should have been on at least the first patent!

Why would Prof Calos and Stanford University fight so hard against their former student, who clearly contributed enough to the invention to appear on the original patent application? Is splitting the royalties from one patent with one extra person, a student who contributed to the work, so terribly painful? Stanford’s policy is to divide the royalties (after paying for the patenting and lawyer fees) 1/3 to the inventors, 1/3 to the department, and 1/3 to the school. So the prof loses half of her royalties by re-including her former student as an inventor, but the University loses nothing.

Is the recent patent application plagiarized from the student’s dissertation? Only if the dissertation was not first self-plagiarized from an earlier paper. Who knows. Regarding the plagiarism complaint, Stanford had this to say:

“I think we’ve really done our part at this point,” Dunkley said. “The inventorship has been corrected. He has been made whole for any amount that he would have received if he had been an inventor from the beginning. So from the University’s perspective, all necessary action has been taken to rectify any differences on the inventorship issue.” (source: Stanford Daily)

That’s not really very satisfying. What if the roles were reversed and a student copied significant portions of his PI’s earlier grant proposal into his dissertation without the PI’s permission? Or submitted a paper without the PI’s knowledge? That student would probably be kicked out of Stanford at a minimum. The least the University could do is investigate this case and if Prof Calos has a history of taking credit for other peoples’ work. Maybe Prof Calos is innocent and the student is trying to steal credit, but it would be nice if the University would check into it.

All in all, the entire situation is not clear-cut. I suspect that the whole incident is the result of large egos, hurt feelings, and greed—from all parties! This is why it is very important to not burn bridges and to try to empathize with your PI or your student. I suspect this conflict could have been resolved early on if all parties had been more understanding and willing to listen and compromise.

Bottom line though, I find it unfortunate that the University would fight one of its own students.

P.S. Guess what Sclimenti is doing now?

quake’s genome

Steve Quake sequenced his own genome. Cute.

you don’t understand how karma works

A former employee at SLAC intentionally destroyed thousands of protein crystals. Fortunately, only a couple hundred had not already been measured. You can read about it at C&E News or SF Chronicle.

Apparently, she claims that she wanted to reset her bad karma by harming her boss who had fired her (for not showing up to work for weeks). That’s not karma, that’s vengence.

We don’t know the entire story; maybe her boss was a real jackass. Regardless, she acheived vengence upon her boss by harming many other people—who had spent their research time crystallizing those proteins. That’s not very considerate.

They let this crazy woman in and Charles can’t even get past the gate at SLAC when he’s invited there!

UPDATE: She’s missing!

looking forward to wolfram|alpha

Wolfram|alpha search engine goes live on Monday. I can’t wait. Here’s a demo. I’m sure they selected the queries very carefully. But for the queries they ran, Wolfram|alpha looks awesome!

There will be a live broadcast of them trying to go online, starting at 8 PM EST (5 PM Pacific).

UPDATE: Try using the site for chemistry.

first x-ray laser

The first x-ray laser went on-line last week at SLAC. I just saw a talk with the lasing data. Cool!

New “Not-Science” Website

I’m pleased to announce the newest addition to the everdayscientist.com community, a new political website called Havenworks.com – a News “Haven” for Political “Works”.  I’ve decided to move away from WordPress and try my hand at some real website designing, and I do think I’ve done a good job.  I hope you like it!

Havenworks.com

ask not…

In honor of Barack Obama’s inauguration today, I would like to quote the ravings of a homeless man I heard in the street last night:

John F. Kennedy! John F. Kennedy! Ask not what he can do for your country. Ask for what you got!

Good luck, President Obama.

JACSes’s new cover!

Holy crap! JACS has decided to put art on its covers!!!!1!!

I think that’s a terrible idea. JACS was the only major chemistry journal not to frill up its cover with some bullshit pictures of some pseudosciencey research. Now it’ll probably go the way of Angewandte and have penguins and shit on its covers.

JACS used to be the classy journal of chemistry—a real gentleman’s journal. Now it’s just another noisy mag on the shelf. I encourage ACS to reverse their decision to deflower their flagship journal.

All the JACSβ stuff on the website is cool. If you want to make a JACS Facebook page and have podcasts where someone reads an entire paper word-for-word, that’s fine with me. Even the image challenges are cool (even though I get 90% of them wrong because I don’t have the patience to read all the options). But stay away from the beautiful, clean cover.

Maybe Google should change their homepage to look like Excite?

steve chu as SOE

So it looks like Obama has snagged Steve Chu for Secretary of Energy.

Officials familiar with the selections say Mr. Chu is likely to focus his attention on the Energy Department’s core missions: basic science, nuclear weapons and cleaning up a nuclear-weapons manufacturing complex contaminated since the Cold War.

Sounds good. Steve is a big name in my field, so I know his work well. In fact, I even worked in his lab for a summer REU. He’s a nice guy and a good scientist. I haven’t been following his policy work very closely, but I suspect that he’s got some good ideas. Regardless, I really like the idea of a real, live scientist as SOE!

UPDATE: Here’s a NYT summary of Steve. Also, here’s an interview he gave about his thoughts on policy at Berkeley.

acs feeds lost images

I’m fine with the ACS redesign. What I’m not fine with is no longer having the TOC images in my RSS feeds from ACS. What are they thinking?!? Hopefully that gets fixed soon.

UPDATE:

I received this email from ACS:

We are aware that the journal RSS feeds are currently not displaying the TOC graphics that were present before we moved to our new Web platform. Please be patient as we work to bring these graphics back to the feeds. Thank you for voicing your concerns and making sure that we recognize their importance. We truly value your feedback and hope that this will be resolved soon.

So we need to be patient.

UPDATE 2: The images returned, but they’re so small to be worthless. I used Yahoo Pipes to edit the feed to show the “medium” images. Here’s the new JACS RSS feed with medium images.

UPDATE 3: Looks like everything is fixed finally. No need for my Yahoo! Pipes edits anymore.